Workshop Timetable

Day 1 - Fri 23rd Oct

• 9.00 Arrive
  • Pre-workshop questionnaire
• 9.30 - 10.30 Lectures
  • Overview of Adv. Sampling and Intro to LSDMap / DM-d-MD (CC),
  • Intro to COCO (CL)
• 10.30 - 11.00 Coffee Break
• 11.00 - 12.30 Practical - Running ExTASY workflows on ARCHER (IB)
  • ExTASY User guide / Tutorial Documentation
  • Setup instructions
• 12.30 - 13.30 Lunch
• 13.30 - 15.00 Practical - Using and extending ExTASY workflows (AS)
  • Tutorial on CoCo/Amber followed by...
  • the hybrid combination of custom generated kernels with ExTASY available ones, as examples to extend ExTASY. The gromacs/coco workflow will be showcased for this purpose.
  • Tutorial on LSDMap / DM-d-MD is also available for those who are interested
• 15.00 - 15.30 Coffee Break
• 15.30 - 17.00 Practical - Sampling other systems with ExTASY (AS)
• 17.00 Finish
  • Post-workshop questionnaire

Day 2 - Sat 24th Oct

• 9:30 - 10:30 Lectures: Introduction to Markov state modeling and PyEMMA (www.pyemma.org)
• 10:30 - 11:00 Coffee break
• 11:00 - 12:30 Practical - Reading MD data, Featurizing, time-lagged indpendent component analysis (TICA) and Clustering
• 12:30 - 13:30 Lunch
• 13:30 - 15:00 Practical - Markov state model estimation and analysis
• 15:00 - 15:30 Coffee breach
• 15:30 - 17:00 Practical - Coarse-graining of Markov state models, Hidden Markov models and Transition path theory (TPT)
• 17:00 Finish